Identificación y caracterización in silico de la zona de interación entre el péptido beta-amiloide y compuestos derivados del naftaleno by Alberto Bencomo-Martínez, Marquiza Sablón-Carrazana, Suchitil Rivera-Marrero, Chryslaine Rodríguez-Tanty, Yoanna María Álvarez-Ginarte, Amaury Pupo-Meriño

“…Las simulaciones fueron hechas contra las 10 configuraciones de RMN del Aβ tomadas del Protein Data Bank (PDB, código 1IYT). Con el objetivo de validar este procedimiento se reprodujo satisfactoriamente la afinidad entre la estructura reportada del Aβ y los pentapéptidos GVVIA y RVVIA. …”
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Protein Binder (ProBi) as a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution by Phuong Ngoc Pham, Maroš Huličiak, Lada Biedermannová, Jiří Černý, Tatsiana Charnavets, Gustavo Fuertes, Štěpán Herynek, Lucie Kolářová, Petr Kolenko, Jiří Pavlíček, Jiří Zahradník, Pavel Mikulecky, Bohdan Schneider

“…We hereby describe a process based on an analysis of protein structures from the Protein Data Bank and their experimental examination. The candidate protein scaffolds were subjected to a thorough screening including computational evaluation of the mutability, and experimental determination of their expression yield in <i>E. coli</i>, solubility, and thermostability. …”
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Development of a novel prediction model based on protein structure for identifying RPE65-associated inherited retinal disease (IRDs) of missense variants by Jiawen Wu, Zhongmou Sun, Dao wei Zhang, Hong-Li Liu, Ting Li, Shenghai Zhang, Jihong Wu

“…The three-dimensional structure of RPE65 was retrieved from the Protein Data Bank (PDB) and modified with Pymol software. …”
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Cheminformatics and Machine Learning Approaches to Assess Aquatic Toxicity Profiles of Fullerene Derivatives by Natalja Fjodorova, Marjana Novič, Katja Venko, Bakhtiyor Rasulev, Melek Türker Saçan, Gulcin Tugcu, Safiye Sağ Erdem, Alla P. Toropova, Andrey A. Toropov

“…First, we analyzed the binding affinity of 169 FDs to 10 human proteins (1D6U, 1E3K, 1GOS, 1GS4, 1H82, 1OG5, 1UOM, 2F9Q, 2J0D, 3ERT) obtained from the Protein Data Bank (PDB) and showing high similarity to proteins from aquatic species. …”
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Synthesis, In Silico Study, Antibacterial and Antifungal Activities of <i>N</i>-phenylbenzamides by Melanny Ika Sulistyowaty, Galih Satrio Putra, Tutuk Budiati, Anastasia Wheni Indrianingsih, Farida Anwari, Dini Kesuma, Katsuyoshi Matsunami, Takayasu Yamauchi

“…ADMET predictions used pkCSM software online, while the docking studies used MVD software (Molegro ^® Virtual Docker version 5.5) on Aminoglycosid-2 ″-phosphotransferase-IIa (APH2 ″-IIa) enzyme with protein data bank (PDB) ID code 3HAV as antibacterial and aspartic proteinases enzyme (Saps) with PDB ID code 2QZX as an antifungal. …”
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Synthesis and Biological Evaluation of Novel Triple-Modified Colchicine Derivatives as Potent Tubulin-Targeting Anticancer Agents by Urszula Majcher, Greta Klejborowska, Magdalena Kaik, Ewa Maj, Joanna Wietrzyk, Mahshad Moshari, Jordane Preto, Jack A. Tuszynski, Adam Huczyński

“…Additionally, the mode of binding of the synthesized compounds was evaluated in silico using molecular docking to a 3D structure of &#946;-tubulin based on crystallographic data from the Protein Data Bank and homology methodology. Binding free energy estimates, binding poses, and MlogP values of the compounds were obtained. …”
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Modeling and Molecular Dynamic Simulation of F(ab′) Fragment of Nimotuzumab for Lung Cancer Diagnostics by Yurika Sastyarina, Ade Rizqi Ridwan Firdaus, Zuhrotun Nafisah, Ari Hardianto, Muhammad Yusuf, Martalena Ramli, Abdul Mutalib, Ukun MS Soedjanaatmadja

“…The crystal structure of Fab of nimotuzumab from protein data bank was used as a template to construct the model of F(ab′) 2 . …”
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Insilico Screening for Identification of Hits against SARS-Cov-2 Variant of Concern B.1.617 and NSP12 Mutants by Molecular Docking and Simulation Studies by Madishetti Vinuthna Vani, Reddy Sudhakar, kalagara Sudhakar, Garg Ashish, Enaganti Sreenivas, Hussain Sardar

“…The three-dimensional structures of NSPs and S Spike proteins were retrieved from the protein data bank or modeled. And a dataset of an antiviral compound library containing 490,000 drug-like ligands and structurally diverse biologically active scaffolds was used for our studies. …”
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Macroalgae Bioactive Compounds for the Potential Antiviral of SARS-CoV-2: An In Silico Study by Hasriaton Padmi, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Mada Triandala Sibero, Muhammad Hermawan Widyananda, Md. Emdad Ullah, Olga Gumenyuk, Svetlana Chylichcova, Natalia Bratishko, Eka Sunarwidhi Prasedya, Teguh Hari Sucipto, Rahadian Zainul

“…Twenty-seven macroalgae compounds were obtained from PubChem (NCBI, USA), while target protein ACE2 receptor was collected from Protein Data Bank (PDB). Then the initial screening study drug-likeness conducted by Lipinski rule of five web server and prediction of bioactive probability carried out by PASS (Prediction of activity spectra for biologically active substances) Online web server. …”
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VIRTUAL SCREENING: IDENTIFICATION OF COMPOUNDS WITH POSSIBLE QUORUM SENSING AGONISTIC ACTIVITY IN Pseudomonas aeruginosa by Maicol Ahumedo, Margarita Velásquez, Ricardo Vivas Reyes

“…Methods: The structure of the receptor was taken from the Protein Data Bank (PDB). The program AutoDock 4.2 was used to perform docking calculations. …”
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Heterologous expression of Plasmodium vivax apical membrane antigen 1 (PvAMA1) for binding peptide selection by Ching Hoong Chew, Yvonne Ai Lian Lim, Kek Heng Chua

“…The binding sites of each selected peptides toward PvAMA1 (Protein Data Bank, PDB ID: 1W8K) were in silico predicted using CABS-dock web server. …”
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Discovery of Potential Antiviral Compounds against Hendra Virus by Targeting Its Receptor-Binding Protein (G) Using Computational Approaches by Faisal Ahmad, Aqel Albutti, Muhammad Hamza Tariq, Ghufranud Din, Muhammad Tahir ul Qamar, Sajjad Ahmad

“…Briefly, a library of 6000 antiviral compounds was screened for potential drug-like properties, followed by the molecular docking of short-listed compounds with the Protein Data Bank (PDB) structure of Ggp. Docked complexes of top two hits, having maximum binding affinities with the active sites of Ggp, were further considered for molecular dynamic simulations of 200 ns to elucidate the results of molecular docking analysis. …”
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ESTUDO COMPARATIVO DE DOCKING MOLECULAR ENTRE O INIBIDOR DE PROTEASE SAQUINAVIR E O CAROTENOIDE BIXINA COMO POTENCIAL INIBIDOR DO VÍRUS HIV TIPO I (1HXB) by Jacilene Silva, Marcia Machado Marinho, José Elieudo da Silva, Emanuelle Machado Marinho, Emmanuel Silva Marinho

“…A metodologia se desenvolveu em 5 etapas: obtenção da estrutura do ligante Bixina no repositório ChemSpider; obtenção da estrutura proteica do HIV-1 no repositório Protein Data Bank; otimização do ligante por meio do software Mopac; preparação do ligante e da proteína por meio do software AutoDockTools; Docking Molecular. …”
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The apo-structure of the leucine sensor Sestrin2 is still elusive by Saxton, Robert Andrew, Knockenhauer, Kevin Edward, Schwartz, Thomas, Sabatini, David

“…We recently reported the structure of Sestrin2 in complex with leucine [Protein Data Bank (PDB) ID, 5DJ4] and demonstrated that mutations in the leucine-binding pocket that alter the affinity of Sestrin2 for leucine result in a corresponding change in the leucine sensitivity of mTORC1 in cells. …”
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Matriarch: A Python Library for Materials Architecture by Spivak, David I., Giesa, Tristan, Jagadeesan, Ravi, Buehler, Markus J

“…It is a domain-specific language that gives the user the ability to create almost arbitrary structures with arbitrary amino acid sequences and, from them, generate Protein Data Bank (PDB) files. In this way, Matriarch is more powerful than commercial software now available. …”
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Comprehensive assessment of cancer missense mutation clustering in protein structures by Kamburov, Atanas, Polak, Paz, Lage, Kasper, Lawrence, Michael, Leshchiner, Ignaty, Golub, Todd, Lander, Eric Steven, Getz, Gad Asher

“…We applied this approach to systematically analyze the PanCancer compendium of somatic mutations from 4,742 tumors relative to all known 3D structures of human proteins in the Protein Data Bank. We detected significant 3D clustering of missense mutations in several previously known oncoproteins including HRAS, EGFR, and PIK3CA. …”
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Design of selective peptide inhibitors of anti-apoptotic Bfl-1 using experimental screening, structure-based design, and data-driven modeling by Jenson, Justin Michael

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Molecular display of synthetic oligonucleotide libraries and their analysis with high throughput DNA sequencing by Larman, Harry Benjamin

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Computational studies of protein dynamics and dynamic similarity by Munz, M

“…<p>At the time of writing this thesis, the complete genomes of more than 180 organisms have been sequenced and more than 80000 biological macromolecular structures are available in the Protein Data Bank (PDB). While the number of sequenced genomes and solved three-dimensional structures are rapidly increasing, the functional annotation of protein sequences and structures is a much slower process, mostly because the experimental de-termination of protein function is expensive and time-consuming. …”

Heterologous expression of Plasmodium vivax apical membrane antigen 1 (PvAMA1) for binding peptide selection by Chew, C.H., Lim, Yvonne Ai Lian, Chua, Kek Heng

“…The binding sites of each selected peptides toward PvAMA1 (Protein Data Bank, PDB ID: 1W8K) were in silico predicted using CABS-dock web server. …”